Maher and City Manager Clay Phillips confirmed the decision in separate interviews Thursday. Assistant Chief Cory Moles has been named acting chief.

An email announcing the chief’s leave was sent Thursday afternoon to the mayor, City Council members and city employees, Phillips said.

Phillips said he could not discuss the situation further because it is a personnel matter. He said it’s unknown how long the chief will be on leave.

Maher said he is not allowed to discuss why he was placed on leave because of a confidentiality order. When asked if the action came as a surprise, Maher said, “Very much so.”

The chief said he was told Wednesday morning that he needed to be at a meeting at 1:30 p.m. at City Hall “for a personnel issue.” He said he didn’t know he was the subject of the meeting.

Maher said Phillips, City Attorney Jeffrey Epp and Human Resources Director Sheryl Bennett attended the meeting in the city manager’s office. He was told immediately that he was being placed on paid administrative leave pending a personnel investigation. After a short discussion, Maher said, he signed a “notice of administrative leave” and left.

He is not allowed to enter his office without the city manager’s permission nor access his work email, Maher said.

No reason for the leave is stated in the notice, the chief said. He was told the investigation was not about him and that it was being done to protect him, Maher said.

Maher said that two weeks ago he took concerns about inappropriate conduct by some Police Department managers to the city manager and city attorney.

Phillips said he could not discuss any possible personnel investigation, but added that “any time there’s a complaint brought about any issue, we look into it. It’s a matter of protocol.”

Mayor Sam Abed said administrative leave is “normal business practice” to ensure that personnel investigations are conducted properly.

“There is no time limit to (the leave) … they have to do it right,” Abed said.

He said he supports the policies of the Police Department, which will continue “no matter who’s in charge.”

Maher, who turned 57 Thursday, was sworn in as Escondido police chief in July 2006. He has been with the department for more than 30 years. His salary is $142,500.

He has faced criticism over the years for his department’s use of DUI and driver’s license checkpoints, which some Latino activists have said unfairly target illegal immigrants. The department also partners with Immigration and Customs Enforcement to identify criminal illegal immigrants. That too has been a target of complaints by activists.

Last month, Maher helped organize a peace march as a show of unity among all city residents. Earlier this year, 45 Latino residents completed the Police Department’s first “Spanish Community Academy,” which educated participants about police operations.